getBM error in the biomaRt R package
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@add30e8f
Last seen 5 days ago
Norway

Hello,

I have a list of transcript ids of gasterosteus aculeatus for which I need to extract the gene names, descriptions and other annotations from biomart. While I am using biomaRt R package and the getBM function I am getting the following error

Error in .processResults(postRes, mart = mart, hostURLsep = sep, fullXmlQuery = fullXmlQuery,  : 
  Query ERROR: caught BioMart::Exception::Usage: Filter NA NOT FOUND

It seems that newest versions of biomaRt package cannot run.

My script is as follows

ensembl=useMart(biomart="ensembl",dataset="gaculeatus_gene_ensembl") 

TSS25p_D_Ens = getBM(attributes = c('ensembl_gene_id','ensembl_transcript_id','chromosome_name','start_position','end_position','go_id','go_linkage_type'), 
                        filters = 'ensembl_transcript_id',
                        values = TSS25p_D_geneID,
                        mart = ensembl)

The TSS25p_D_Ens file has the ensembl transcripts ID for the species and looks like this:

> TSS25p_D_geneID
[[1]]
[1] "ENSGACT00000010774"

[[2]]
[1] "ENSGACT00000016763"

[[3]]
[1] "ENSGACT00000022831"


> ensembl
Object of class 'Mart':
  Using the ENSEMBL_MART_ENSEMBL BioMart database
  Using the gaculeatus_gene_ensembl dataset

Because I cannot understand what I am running wrong could someone help?

Thank you in advance. Arun

Annotation • 226 views
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Mike Smith ★ 5.2k
@mike-smith
Last seen 7 minutes ago
EMBL Heidelberg / de.NBI

I think the values argument is expecting a vector of transcript IDs, not a list. Does it work if you try values = unlist(TSS25p_D_geneID) ?

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Hello Mike,

It's working!

Thank you so much.

Cheers, Arun

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